We survey recent progress in the math.matical modelling and simulation of essential molecular dynamics. Particular emphasis is put on computational drug design wherein time-scales of milliseconds up to minutes play th...
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ISBN:
(纸本)0898715598
We survey recent progress in the math.matical modelling and simulation of essential molecular dynamics. Particular emphasis is put on computational drug design wherein time-scales of milliseconds up to minutes play the dominant role. Classical long-term molecular dynamics computations, however, would run into illconditioned initial-value problems already after time-spans of only psec = 10-12 sec. Therefore, in order to obtain results for times of pharmaceutical interest, a combined deterministic-stochastic model is needed. The concept advocated in this paper is the direct identification of metastable conformations together with their life times and their transition patterns. It can be interpreted as a transfer-operator approach corresponding to some underlying hybrid Monte Carlo process, wherein short-term trajectories enter. The spatial discretization of this operator is a hard problem of its own. In order to avoid the 'curse of dimension', the construction of appropriate spatial boxes requires careful consideration. Once this operator has been discretised a stochastic matrix arises. This matrix is then treated by Perron cluster analysis, a recently developed cluster analysis method involving the numerical solution of an eigenproblem for a cluster of eigenvalues called the Perron cluster. As a biomolecular example we present a rather recent SARS protease inhibitor.
An increasing number of distributed applications are currently being constructed as sets of connected components and dynamically deployed in wide area networks using frameworks such as CORBA, .NET, and Web Services. S...
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ISBN:
(纸本)0769521320
An increasing number of distributed applications are currently being constructed as sets of connected components and dynamically deployed in wide area networks using frameworks such as CORBA, .NET, and Web Services. Such dynamic deployments enable applications to flexibly adapt to changes in client QoS requirements and network properties, but introduce a consistency problem because of replicated components. Ideally, the frameworks deploying the applications should ensure that the application consistency requirements are satisfied, even though the requirements can range from weak to strong and dynamically change at run-time. Thus, a key challenge is to design a flexible cache coherence protocol that uses application-specific information while still being application-neutral. This paper describes Piece, an application-neutral cache coherence protocol used by a component-based framework (Partitionable Services Framework) to satisfy the consistency requirements of deployed applications. Piece allows applications to specify appropriate consistency and granularity levels and define complex synchronization decisions as simple functions. We demonstrate the benefits of our cache coherence protocol by analyzing the behavior of a component-based application modeling an airline reservation system.
The uniform persistence is proved for a non-autonomous competitive and prey-predator model with ratio-dependent functional response and stage-structure. By constructing a Liapunov functional, we establish the conditio...
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The uniform persistence is proved for a non-autonomous competitive and prey-predator model with ratio-dependent functional response and stage-structure. By constructing a Liapunov functional, we establish the conditions of existence and uniqueness for the positive periodic solution, which is globally asymptotically stable. We get a unique almost periodic solution for an almost periodic system as well under corresponding conditions .by means of the Razumikhin function method.
TCP performance degrades significantly in mobile ad hoc networks because most of packet losses occur as a result of route failures. Prior work proposed to provide link failure feedback to TCP so that TCP can avoid res...
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ISBN:
(纸本)9781581138689
TCP performance degrades significantly in mobile ad hoc networks because most of packet losses occur as a result of route failures. Prior work proposed to provide link failure feedback to TCP so that TCP can avoid responding to route failures as if congestion had occurred. However, after a link failure is detected, several packets will be dropped from the network interface queue;TCP will time out because of these losses. It will also time out for ACK losses caused by route failures. In this paper, we propose to make routing protocols aware of lost data packets and ACKs and help reduce TCP timeouts for mobility-induced losses. Toward this end, we present two mechanisms: early packet loss notification (EPLN) and best-effort ACK delivery (BEAD). EPLN seeks to notify TCP senders about lost data packets. For lost ACKs, BEAD attempts to retransmit ACKs at either intermediate nodes or TCP receivers. Both mechanisms extensively use cached routes, without initiating route discoveries at any intermediate node. We evaluate TCP-ELFN enhanced with the two mechanisms using two caching strategies for DSR, path caches and a distributed cache update algorithm proposed in our prior work. We show that TCP-ELFN with EPLN and BEAD significantly outperforms TCP-ELFN under both caching strategies. We conclude that cross-layer information awareness is key to making TCP efficient in the presence of mobility.
We study the problem of computing the visibility graph defined by a set P of n points inside a polygon Q: two points p, q Ε P are joined by an edge if the segment pq ⊂ Q. Efficient output-sensitive algorithms are kno...
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We study the problem of computing the visibility graph defined by a set P of n points inside a polygon Q: two points p, q Ε P are joined by an edge if the segment pq ⊂ Q. Efficient output-sensitive algorithms are known for the case in which P is the set of all vertices of Q. We examine the general case in which P is an arbitrary set of points, interior or on the boundary of Q and study a variety of algorithmic questions. We give an output-sensitive algorithm, which is nearly optimal, when Q is a simple polygon. We introduce a notion of "fat" or "robust" visibility, and give a nearly optimal algorithm for computing visibility graphs according to it, in polygons Q that may have holes. Other results include an algorithm to detect if there are any visible pairs among P, and algorithms for output-sensitive computation of visibility graphs with distance restrictions, invisibility graphs, and rectangle visibility graphs.
Fuzzy Extension Matrix induction is an extraction technique of fuzzy rules, which can be used in handling ambiguous classification problems related to human's thought and sense. The entire process of building heur...
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ISBN:
(纸本)0780384032
Fuzzy Extension Matrix induction is an extraction technique of fuzzy rules, which can be used in handling ambiguous classification problems related to human's thought and sense. The entire process of building heuristic algorithm based on Fuzzy Extension Matrix is dependent of three specified parameters that seriously affect the computational effort and the rule extraction accuracy. Since the value of three parameters is usually given in terms of human experience or real requirements, it is very difficult to determine its optimal value. This paper makes an initial attempt to give some guidelines of how to automatically choose these parameters by analyzing the relationship between the values of parameters and the number of rules generated.
We revisit the problem of computing shortest obstacle-avoiding paths among obstacles in three dimensions. We prove new hardness results, showing, e.g., that computing Euclidean shortest paths among sets of "stack...
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We revisit the problem of computing shortest obstacle-avoiding paths among obstacles in three dimensions. We prove new hardness results, showing, e.g., that computing Euclidean shortest paths among sets of "stacked" axis-aligned rectangles is NP-complete, and that computing L 1-shortest paths among disjoint balls is NP-complete. On the positive side, we present an efficient algorithm for computing an L 1shortest path between two given points that lies on or above a given polyhedral terrain. We also give polynomial-time algorithms for some versions of stacked polygonal obstacles that are "terrain-like" and analyze the complexity of shortest path maps in the presence of parallel halfplane "walls".
Decision trees and extension matrixes are two methodologies for (fuzzy) rule generation. This paper gives an initial study on the comparison between the two methodologies. Their computational complexity and the qualit...
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ISBN:
(纸本)0780384032
Decision trees and extension matrixes are two methodologies for (fuzzy) rule generation. This paper gives an initial study on the comparison between the two methodologies. Their computational complexity and the quality of rule generation are analyzed. The experimental results show that the number of generated rules of the heuristic algorithm based on extension matrix is fewer than the decision tree algorithm. Moreover, regarding the testing accuracy (i.e., the generalization capability for unknown cases), experiments also show that the extension matrix method is better than the other.
This paper addresses the problem of piecewise linear approximation of implicit surfaces. We first give a criterion ensuring that the zero-set of a smooth function and the one of a piecewise linear approximation of it ...
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This paper addresses the problem of piecewise linear approximation of implicit surfaces. We first give a criterion ensuring that the zero-set of a smooth function and the one of a piecewise linear approximation of it are isotopic. Then, we deduce from this criterion an implicit surface meshing algorithm certifying that the output mesh is isotopic to the actual implicit surface. This is the first algorithm achieving this goal in a provably correct way.
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